Uses of Package
org.biojava.bio.search

Packages that use org.biojava.bio.search

org.biojava.bio.program.sax	Parsers which offer XML representations of the output from common bioinformatics tools.
org.biojava.bio.program.ssbind	Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
org.biojava.bio.search	Interfaces and classes for representing sequence similarity search results.

Classes in org.biojava.bio.search used by org.biojava.bio.program.sax

SearchContentHandler
SearchContentHandler is a notification interface for objects which listen to search stream parsers.

Classes in org.biojava.bio.search used by org.biojava.bio.program.ssbind

SearchBuilder
The SearchBuilder interface is to be used by objects which accumulate state via a SearchContentHandler and then construct a SeqSimilaritySearchResult object.

SearchContentHandler
SearchContentHandler is a notification interface for objects which listen to search stream parsers.

SeqSimilaritySearchResult
Objects of this type represent one particular result of a sequence similarity search.

Classes in org.biojava.bio.search used by org.biojava.bio.search

BioMatcher
Interface for things that perform matches.

BioPattern

BlastLikeSearchFilter
A SearchContentHandler class that implements filtering in chains of SearchContentHandler instances.

BlastLikeSearchFilter.AbstractBlastLikeSearchFilter

BlastLikeSearchFilter.ByHitProperty
Applies test to the value specified by the key in hit properties.

BlastLikeSearchFilter.BySearchProperty
Applies test to the value specified by the key in search properties.

BlastLikeSearchFilter.BySubHitProperty
Applies test to the value specified by the key in subhit properties.

BlastLikeSearchFilter.Node

FilterTest
Class for implementing tests with BlastLikeSearchFilter objects.

SearchContentAdapter
An adapter for SearchContentHandler.

SearchContentHandler
SearchContentHandler is a notification interface for objects which listen to search stream parsers.

SeqSimilaritySearchHit
Objects of this type represent one particular hit (sequence and associated information) from a sequence similarity search.

SeqSimilaritySearchHit.ByScoreComparator
ByScoreComparator compares SeqSimilaritySearchHits by their score.

SeqSimilaritySearchHit.BySubHitCountComparator
BySubHitCountComparator compares SeqSimilaritySearchHits by their number of sub-hits.

SeqSimilaritySearchResult
Objects of this type represent one particular result of a sequence similarity search.

SeqSimilaritySearchSubHit
Objects of this type represent one particular sub-hit (one concrete sequence stretch within a sequence and associated information) from a sequence similarity search hit.

SeqSimilaritySearchSubHit.ByScoreComparator
ByScoreComparator compares SeqSimilaritySearchSubHits by their score.

SeqSimilaritySearchSubHit.BySubjectStartComparator
BySubjectStartComparator compares SeqSimilaritySearchSubHits by their start position on the subject sequence.